Variant report

Variant	rs771460
Chromosome Location	chr1:93817818-93817819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr1:93817795-93817978	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93816828..93819255-chr1:93822966..93824578,2	MCF-7	breast:
2	chr1:93717824..93719584-chr1:93817437..93819207,2	K562	blood:

Variant related genes	Relation type
DR1	TF binding region

Extended variants
information (count: 133 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1000606	0.90[EUR][1000 genomes]
rs10430073	0.90[EUR][1000 genomes]
rs10782958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1081523	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1081524	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1081525	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1081526	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10874765	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10874767	0.92[EUR][1000 genomes]
rs10874771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10874774	0.87[EUR][1000 genomes]
rs10874775	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1088319	0.82[EUR][1000 genomes]
rs11164878	0.87[AMR][1000 genomes]
rs11164882	0.87[AMR][1000 genomes]
rs11164888	0.92[EUR][1000 genomes]
rs11164889	0.92[EUR][1000 genomes]
rs11164890	0.92[EUR][1000 genomes]
rs11164891	0.88[EUR][1000 genomes]
rs11164906	0.90[EUR][1000 genomes]
rs11164911	0.96[EUR][1000 genomes]
rs11582703	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11584466	0.90[EUR][1000 genomes]
rs12070900	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12071627	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12080715	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12085959	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12088338	0.84[AMR][1000 genomes]
rs12090723	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731809	0.93[EUR][1000 genomes]
rs1323626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1323627	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1323628	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1414367	0.87[AMR][1000 genomes]
rs1535698	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1535700	0.97[EUR][1000 genomes]
rs1570528	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2031223	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2031224	0.90[EUR][1000 genomes]
rs2104280	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2484485	0.87[AMR][1000 genomes]
rs2783492	0.87[AMR][1000 genomes]
rs2783498	0.87[AMR][1000 genomes]
rs2783506	0.87[AMR][1000 genomes]
rs2815408	0.87[AMR][1000 genomes]
rs2815409	0.87[AMR][1000 genomes]
rs2815410	0.87[AMR][1000 genomes]
rs2815411	0.87[AMR][1000 genomes]
rs2815412	0.84[AMR][1000 genomes]
rs4573531	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847239	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4847407	0.91[EUR][1000 genomes]
rs4847409	0.90[EUR][1000 genomes]
rs4847411	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs485622	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs488646	0.90[EUR][1000 genomes]
rs504810	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs505531	0.87[AMR][1000 genomes]
rs508942	0.89[EUR][1000 genomes]
rs512361	0.90[EUR][1000 genomes]
rs519723	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs523262	0.89[EUR][1000 genomes]
rs546	0.87[AMR][1000 genomes]
rs556888	0.90[EUR][1000 genomes]
rs558667	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs559397	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56303209	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs566743	0.86[EUR][1000 genomes]
rs571212	0.83[EUR][1000 genomes]
rs587754	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs605759	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs626714	0.92[EUR][1000 genomes]
rs628714	0.88[EUR][1000 genomes]
rs629153	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631966	0.90[EUR][1000 genomes]
rs633789	0.90[EUR][1000 genomes]
rs637198	0.89[EUR][1000 genomes]
rs641390	0.89[EUR][1000 genomes]
rs6541351	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541400	0.90[EUR][1000 genomes]
rs658178	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs661566	0.84[EUR][1000 genomes]
rs662546	0.84[EUR][1000 genomes]
rs6657587	0.92[EUR][1000 genomes]
rs6664886	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6667701	0.92[EUR][1000 genomes]
rs667680	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6687359	0.90[EUR][1000 genomes]
rs668944	0.88[EUR][1000 genomes]
rs6701250	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs670650	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs671559	0.87[AMR][1000 genomes]
rs693872	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7413775	0.90[EUR][1000 genomes]
rs7519163	0.90[EUR][1000 genomes]
rs7525189	0.90[EUR][1000 genomes]
rs7529639	0.92[EUR][1000 genomes]
rs7546661	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7551635	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7555292	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771448	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771449	0.92[EUR][1000 genomes]
rs771450	0.92[EUR][1000 genomes]
rs771451	0.92[EUR][1000 genomes]
rs771452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771453	0.92[EUR][1000 genomes]
rs771455	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs771456	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771457	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771459	0.92[EUR][1000 genomes]
rs771463	0.96[EUR][1000 genomes]
rs771464	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771466	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771467	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771468	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771469	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771471	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771475	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771477	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs797660	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs797669	0.84[EUR][1000 genomes]
rs809515	0.83[EUR][1000 genomes]
rs810028	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs812789	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9432680	0.89[EUR][1000 genomes]
rs9432700	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9432701	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs771460	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs771460	RP4-717I23.3	cis	Artery Tibial	GTEx
rs771460	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs771460	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs771460	RP4-717I23.3	cis	Stomach	GTEx
rs771460	RP4-717I23.3	cis	lung	GTEx
rs771460	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs771460	RP4-717I23.3	cis	Whole Blood	GTEx
rs771460	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs771460	RP4-717I23.3	cis	Thyroid	GTEx
rs771460	RP4-717I23.3	cis	Artery Aorta	GTEx
rs771460	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs771460	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs771460	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93812800-93823800	Weak transcription	Spleen	Spleen
2	chr1:93812800-93831000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93812800-93832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:93813000-93823800	Weak transcription	Gastric	stomach
5	chr1:93813400-93820200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:93814200-93819200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:93814200-93823600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:93814200-93823800	Weak transcription	Right Ventricle	heart
11	chr1:93814400-93818000	Weak transcription	Placenta	Placenta
12	chr1:93814600-93819600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:93814800-93820400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:93815000-93820200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:93815200-93818400	Enhancers	Brain Substantia Nigra	brain
16	chr1:93815200-93819400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:93815200-93821800	Weak transcription	Fetal Stomach	stomach
18	chr1:93815400-93819400	Weak transcription	A549	lung
19	chr1:93815400-93839800	Weak transcription	Aorta	Aorta
20	chr1:93815600-93818400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:93815600-93818400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:93815600-93818400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:93815600-93818400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:93815600-93818600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:93815600-93819000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:93815600-93819200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:93815600-93819600	Enhancers	Adipose Nuclei	Adipose
28	chr1:93815600-93820000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:93815600-93820200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:93815600-93821000	Weak transcription	Brain Germinal Matrix	brain
31	chr1:93815600-93834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:93815800-93818000	Enhancers	Small Intestine	intestine
33	chr1:93815800-93818200	Weak transcription	Fetal Kidney	kidney
34	chr1:93815800-93819400	Enhancers	Primary T cells from cord blood	blood
35	chr1:93815800-93819400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:93816000-93818000	Weak transcription	Fetal Heart	heart
37	chr1:93816000-93818200	Enhancers	Hela-S3	cervix
38	chr1:93816000-93818400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:93816000-93818800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:93816000-93819000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:93816000-93819600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:93816000-93819600	Enhancers	NHDF-Ad	bronchial
43	chr1:93816000-93823800	Weak transcription	Stomach Mucosa	stomach
44	chr1:93816000-93832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:93816200-93818000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:93816200-93818000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:93816200-93823400	Weak transcription	HSMMtube	muscle
48	chr1:93816400-93818200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:93816400-93818400	Enhancers	HMEC	breast
50	chr1:93816400-93818400	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links